Closed hidvegin closed 2 months ago
These files appear to have undergone some sort of trimming already, but presumably only for adapter but not quality? There are three things I noticed, but I am not sure if any of them are worth looking at specifically, generally the quality is very good.
-a GGGGGGGGGG
should get rid of this.Also you could of course run 2 assemblies, one trimmed, and one 'as-is', and compare :)
Thank @FelixKrueger for your answer and help.
I tried two different parameters for TrimGalore based on your suggestions.
1RS-1BL_Mv179_S1_R1_001_val_1_fastqc.zip 1RS-1BL_Mv179_S1_R2_001_val_2_fastqc.zip 1RS-1BL_Mv179_S1_R1_001.fastq.gz_trimming_report.txt 1RS-1BL_Mv179_S1_R2_001.fastq.gz_trimming_report.txt
-a GGGGGGGGGG --clip_R1 13 --clip_R2 13
These are the results:1RS-1BL_Mv179_S1_R.zip 1RS-1BL_Mv179_S1_R1_001.fastq.gz_trimming_report.txt 1RS-1BL_Mv179_S1_R2_001.fastq.gz_trimming_report.txt
Based on the results, I think I should do two trimming process. First, I should use the default parameters and TrimGalore will cut the Illumina universal adapter. After, I should use the -a GGGGGGGGGG --clip_R1 13 --clip_R2 13
parameters.
What do you think about it?
That looks really quite clean... Just as a comment, you should also be able to do both of these actions in one go, by specifying
trim_galore --paired --clip_R1 13 --clip_R2 13 -a " AGATCGGAAGAGC -a GGGGGGGGGGGGGGG -n 2" -a2 " AGATCGGAAGAGC -a GGGGGGGGGGGGGGG -n 2" file 1 file2
Thank @FelixKrueger for your answer.
Dear @FelixKrueger,
I have got paired-end reads from Illumina sequencer. I analyzed the reads with
fastqc
, but I can not decide that I should trim 5' or 3' end of the R1 or R2 reads. I would like to use this reads for de novo assembly because we do not have any reference genome. I add here the results. Could you help me with this issue?1RS-1BL_Mv179_S1_R1_001_fastqc.zip 1RS-1BL_Mv179_S1_R2_001_fastqc.zip